gatk3=~/tools/StandTools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar
log_path=~/20220915_gastric_multiple/dna_combinePublic/log
tmp_path=~/20220915_gastric_multiple/dna_combinePublic/tmp
ref_fasta=~/ref/seq/GRCh37.fa
out_path=~/20220915_gastric_multiple/dna_combinePublic/gvcf
call_bed=~/20220915_gastric_multiple/dna_combinePublic/gvcf/CDH1_region.bed
input_list=~/20220915_gastric_multiple/dna_combinePublic/gvcf/normalBam.list

java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+PrintFlagsFinal \
-XX:+PrintGCTimeStamps -XX:+PrintGCDateStamps -XX:+PrintGCDetails \
-Xloggc:${log_path}/6snp_gc_log.HaplotypeCaller_20220701.log \
-Xmx450g -Djava.io.tmpdir=${tmp_path}  \
-jar ${gatk3} \
-T HaplotypeCaller --disable_auto_index_creation_and_locking_when_reading_rods \
-R ${ref_fasta}  \
-o ${out_path}/GenotypeGVCFs.vcf.gz \
-I ${input_list} \
-L ${call_bed} \
--minPruning 3 --maxNumHaplotypesInPopulation 200 \
--max_alternate_alleles 20 -variant_index_parameter 128000 \
-variant_index_type LINEAR -contamination 0.0 \
-G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation -A SpanningDeletions -A StrandOddsRatio \
2> ${log_path}/GenotypeGVCFs.log